AMBER Archive (2009)

Subject: Re: [AMBER] atom type no recognize - xleap version 10 but fine in v 9

• Previous message: Ross Walker: "RE: [AMBER] Hard limit in Amber10?"
• In reply to: Peter Gannett: "[AMBER] atom type no recognize - xleap version 10 but fine in v 9"
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On Fri, Jun 19, 2009, Peter Gannett wrote:
>
> I've an odd problem. I have been using the attached files for heme. By
> themselves or apart of P450s, they load fine and permit me to write out
> topology and coordinate files from xleap without complaint (ignoring a
> warning about a short bond and charge not being zero). I tried to use
> these for the same purpose with xleap in amber v10. I can not write
> topology/coordinate files and give me a message (see below) about the
> four heme nitrogens not being recognized (which does not happen in v9 or
> earlier).

The frcmod file has no nonbonded parameters for atom type NP, and you need
those. I have no explanation of the v9/v10 difference.

...dac

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• Previous message: Ross Walker: "RE: [AMBER] Hard limit in Amber10?"
• In reply to: Peter Gannett: "[AMBER] atom type no recognize - xleap version 10 but fine in v 9"
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